Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Quick-install

BiocManager::install(
    "waldronlab/MultiAssayWorkshop", dependencies=TRUE, build_vignettes=TRUE
)

Instructor names and contact information

Marcel Ramos, Ludwig Geistlinger, and Levi Waldron

CUNY School of Public Health

55 West 125th Street

New York, NY 10027

Workshop Description

This workshop demonstrates how to leverage public multi-omics databases, such as the cBioPortal and The Cancer Genome Atlas (TCGA). Workshop participants are given an overview of the cBioPortalData, curatedTCGAData, terraTCGAdata, and SingleCellMultiModal, data packages. It introduces users to minimal data management with MultiAssayExperiment and TCGAutils, packages that organize and manage multi-omics datasets. The workshop will provide participants with ways to improve the ease-of-use of TCGA data, and introduce them to common Bioconductor data classes including SummarizedExperiment, MultiAssayExperiment, and RaggedExperiment. The workshop will also demonstrate the experimental terraTCGAdata package for working with TCGA data on the AnVIL Terra platform, as well as, a review of updates to existing functionality in cBioPortalData, MultiAssayExperiment, TCGAutils, TENxIO, and SingleCellMultiModal.

Keywords: Data Representation, Infrastructure, cBioPortal, MultiOmic Integration

Pre-requisites

• Basic knowledge of R syntax
• Familiarity with the GRanges and SummarizedExperiment classes
• Familiarity with 'omics data types including copy number and gene expression

Workshop Participation

Participants will have a chance to build a MultiAssayExperiment object from scratch, and will also work with data and interfaces from the the curatedTCGAData and cBioPortalData packages.

R/Bioconductor packages used

• MultiAssayExperiment
• RaggedExperiment
• curatedTCGAData
• cBioPortalData
• terraTCGAdata
• SingleCellMultiModal
• TCGAutils
• TENxIO
• UpSetR

Time outline

55 minutes total

Activity	Time
Overview of key packages and data classes	15m
Building a MultiAssayExperiment from scratch	10m
Introduction to curatedTCGAData, cBioPortalData, and terraTCGAdata	10m
Creating and importing TCGA multi-assay datasets	10m
Subsetting and reshaping multi-assay data	10m

Docker Commands for Workshop

The Docker image for this workshop is available on the GitHub Container Registry. Pull (download) the image with the following command:

docker pull ghcr.io/waldronlab/multiassayworkshop:latest

Run the workshop with Docker by using the following command:

docker run -e PASSWORD=bioc -p 8787:8787 ghcr.io/waldronlab/multiassayworkshop:latest

Workshop goals and objectives

Learning goals

• overview common data classes available in Bioconductor
• understand appropriate data structures for different 'omics data types
• explore available functionality in TCGAutils for the management and coordination of multi-omic data
• gain familiarity with cBioPortalData, curatedTCGAData, and terraTCGAdata
• identify advantages of providing integrative data in an analysis-ready platform

Learning objectives

• use curatedTCGAData, cBioPortalData, and terraTCGAdata to create on-the-fly multi-omics data objects
• apply knowledge of MultiAssayExperiment to represent other multi-omics data
• learn about data management techniques such as subsetting, reshaping, growing, and extraction using MultAssayExperiment

Questions & Comments

For more involved / detailed questions, comments, or bug reports, resort to the Bioconductor support site or create an issue on the MultiAssayExperiment issue tracker on GitHub.